I am currently working on a multi-file add-on under Windows, and cannot enable it in User Preferences. What does work is to copy the entire folder into the addons folder, but this will only be my last resort. I have tried two better ways, but unfortunately neither of them work:
Make a shortcut to the folder which contains the script and place it in the add-ons folder. This did work under Linux (shortcut = link), but I have installed a new graphics card which does not like Linux, at least not yet. Presumably Blender considers the .lnk file to be a file rather than a folder.
Press the Install Add-on button and select the python file. This method works for single-file add-ons, but when I select the init.py file nothing happens.
So currently I keep to copies of the add-on; one in Blender’s add-ons folder and one at a permanent location under version control with svn. Alas, this setup is bound to lead to confusion, so it would be nice if this could be avoided.